A lithographic apparatus is a machine that applies a desired pattern onto a substrate, usually onto a target portion of the substrate. A lithographic apparatus can be used, for example, in the manufacture of integrated circuits (ICs). In that instance, a patterning device, which is alternatively referred to as a mask or a reticle, may be used to generate a circuit pattern to be formed on an individual layer of the IC. This pattern can be transferred onto a target portion (e.g. comprising part of, one, or several dies) on a substrate (e.g. a silicon wafer). Transfer of the pattern is typically via imaging onto a layer of radiation-sensitive material (resist) provided on the substrate. In general, a single substrate will contain a network of adjacent target portions that are successively patterned. Known lithographic apparatus include so-called steppers, in which each target portion is irradiated by exposing an entire pattern onto the target portion at one time, and so-called scanners, in which each target portion is irradiated by scanning the pattern through a radiation beam in a given direction (the “scanning”-direction) while synchronously scanning the substrate parallel or anti-parallel to this direction. It is also possible to transfer the pattern from the patterning device to the substrate by imprinting the pattern onto the substrate.
In lithography, a Level Sensor (LS) is used for measuring the substrate height. The substrate height is measured at multiple positions on the substrate, this is done using multiple LS spots (or “measurement spots”) in parallel. Noise and drift in the Level Sensor will deteriorate the accuracy and reproducibility of the measured positions. This noise and drift can be caused by movements of mechanical and optical parts of the LS system, drift and noise of electrical parts of the LS system and changes in the (optical) refractive-index of the media (e.g. air, glass) through which light beams of the LS system pass. All the LS spots can be influenced by these effects, also spots which measure on a reference surface. To separate the noise and drift from the signal introduced by a height change of the substrate, noise and drift are measured independently from the height measurement, using a reference beam as for example described in EP 0 502 583 A1. The signal from the reference beam is subtracted from the measurement spots which measure on the substrate, to correct for the disturbance. This will give a noise-free and drift-free position measurement.
However, there may be a disturbance in the reference beam that is not the same as the disturbance in the measurement beam(s). Reasons for a difference in disturbance of the reference beam with reference to the disturbance of a measurement beam may be:                Time delay of disturbance; the disturbance is not seen at the same time for all LS spots (phase difference between LS spots);        Location of disturbance; very local disturbances in air at the focus point of the LS spots may only be seen by few LS spots;        Movement or deformation of mechanical components in LS will have a different effect on the different LS spots.        